Details of CH4114 (Autumn 2025)
| Level: 4 | Type: Theory | Credits: 4.0 |
| Course Code | Course Name | Instructor(s) |
|---|---|---|
| CH4114 | Molecular Simulation | Susmita Roy |
| Preamble |
|---|
| Preamble: This course will introduce concepts and methods underlying molecular dynamics
simulations of multi-component molecular systems. It should equip one with skills for designing meaningful simulations, data analysis and benchmarking with experimental observations. The course will involve a simulation project in the latter half (*). * The total number of participants will be limited. |
| Syllabus |
|---|
| 1. Introduction to Molecular Simulations
a. History of development b. What is molecular simulation and introduction to Model building c. Introduction to physical/chemical/biological processes of different timescale and length scale 2. Statistical mechanics background a. Microscopic and macroscopic parameters b. Phase space and Ensembles c. Equilibrium and ergodicity 3. Monte Carlo (MC) Simulations (8 Lectures) a. Importance Sampling b. The Metropolis method c. A basic Monte-Carlo Algorithm d. Implementation of Periodic boundary conditions, potential truncation, minimum image convention e. Concept of Reduced Unit and Detailed Balance f. Hands-on sessions on MC sampling 4. Term Project part-I: Model building, MC simulation and data analysis (including phase-analysis of 3D Lennard Jones fluid) 5. Molecular Dynamics (MD) Simulations a. MD Initialization algorithm and hands-on session b. Force calculation algorithm and hands-on session c. Integrating Equation of motion, algorithm and hands-on-session d. Algorithms of different integrators: Verlet, Velocity Verlet, Leapfrog algorithms 6. Molecular dynamics in various Ensembles a. MD at constant temperature; Berendsen, Andersen, and Nos-Hoover Thermostat b. MD at constant pressure: Berendsen, Andersen, and Parrinello-Rahman Barostat 7. Molecular Simulation Analysis Potential energy and Kinetic Energy Measurement of Lennard-Jones fluid, Algorithm of radial distribution function, diffusion, hands-on sessions 8. Term Project-Part II: Model building, MD simulation and data analysis |
| Prerequisite |
|---|
| Basic understanding of thermodynamics and biomolecular structure. Working knowledge of Linux
Suitability: Senior BS-MS students; IPhD students; Research Scholar from both DCS and DBS |
| References |
|---|
| References:
1. Understanding Molecular Simulation: D. Frenkel and B. Smit (Elsevier) 2.Computer Simulations of Liquids, M.P Allen and D.J Tildesley (Oxford) 3. The Art of Molecular Dynamics Simulations: D. C. Rapaport (Cambridge) 4. A Practical Introduction to the Simulation of Molecular Systems, Martin J. Field (Cambridge) |
Course Credit Options
| Sl. No. | Programme | Semester No | Course Choice |
|---|---|---|---|
| 1 | IP | 1 | Not Allowed |
| 2 | IP | 3 | Not Allowed |
| 3 | MP | 1 | Not Allowed |
| 4 | MP | 3 | Elective |
| 5 | MR | 1 | Not Allowed |
| 6 | MR | 3 | Not Allowed |
| 7 | MS | 3 | Not Allowed |
| 8 | MS | 5 | Not Allowed |
| 9 | MS | 7 | Elective |
| 10 | MS | 9 | Elective |
| 11 | RS | 1 | Elective |
| 12 | RS | 2 | Elective |